Document Detail


Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes.
MedLine Citation:
PMID:  23303371     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Understanding the relationship between prokaryotic traits and phylogeny is important for predicting and modeling ecological processes. Microbial extracellular enzymes have a pivotal role in nutrient cycling and the decomposition of organic matter, yet little is known about the phylogenetic distribution of genes encoding these enzymes. In this study, we analyzed 3058 annotated prokaryotic genomes to determine which taxa have the genetic potential to produce alkaline phosphatase, chitinase and β-N-acetyl-glucosaminidase enzymes. We then evaluated the relationship between the genetic potential for enzyme production and 16S rRNA phylogeny using the consenTRAIT algorithm, which calculated the phylogenetic depth and corresponding 16S rRNA sequence identity of clades of potential enzyme producers. Nearly half (49.2%) of the genomes analyzed were found to be capable of extracellular enzyme production, and these were non-randomly distributed across most prokaryotic phyla. On average, clades of potential enzyme-producing organisms had a maximum phylogenetic depth of 0.008004-0.009780, though individual clades varied broadly in both size and depth. These values correspond to a minimum 16S rRNA sequence identity of 98.04-98.40%. The distribution pattern we found is an indication of microdiversity, the occurrence of ecologically or physiologically distinct populations within phylogenetically related groups. Additionally, we found positive correlations among the genes encoding different extracellular enzymes. Our results suggest that the capacity to produce extracellular enzymes varies at relatively fine-scale phylogenetic resolution. This variation is consistent with other traits that require a small number of genes and provides insight into the relationship between taxonomy and traits that may be useful for predicting ecological function.
Authors:
Amy E Zimmerman; Adam C Martiny; Steven D Allison
Publication Detail:
Type:  Journal Article; Research Support, U.S. Gov't, Non-P.H.S.     Date:  2013-01-10
Journal Detail:
Title:  The ISME journal     Volume:  7     ISSN:  1751-7370     ISO Abbreviation:  ISME J     Publication Date:  2013 Jun 
Date Detail:
Created Date:  2013-05-21     Completed Date:  2013-12-19     Revised Date:  2014-06-03    
Medline Journal Info:
Nlm Unique ID:  101301086     Medline TA:  ISME J     Country:  England    
Other Details:
Languages:  eng     Pagination:  1187-99     Citation Subset:  IM    
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MeSH Terms
Descriptor/Qualifier:
Alkaline Phosphatase / genetics
Archaea / enzymology,  genetics*
Bacteria / enzymology,  genetics*
Chitinase / genetics
Ecology
Phylogeny
RNA, Ribosomal, 16S / genetics
beta-N-Acetyl-Galactosaminidase / genetics
Chemical
Reg. No./Substance:
0/RNA, Ribosomal, 16S; EC 3.1.3.1/Alkaline Phosphatase; EC 3.2.1.14/Chitinase; EC 3.2.1.53/beta-N-Acetyl-Galactosaminidase
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